Run name:
Email (optional):
Sequence file: FASTA/FASTQ (compressed or uncompressed) without spaces, parenthesis or other special symbols in the name
Max. 500 MB Download example
Genotyping method: Sommer et al.1 Lighten et al.2 Radwan & Herdegen et al.3,4

1 Sommer S, Courtiol A, Mazzoni CJ. MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout. BMC Genomics. 2013 Aug 9;14:542. [Pubmed]
2 Lighten J, van Oosterhout C, Paterson IG, McMullan M, Bentzen P. Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata). Mol Ecol Resour. 2014 Jul;14(4):753-67. [Pubmed]
3 Radwan J, Zagalska-Neubauer M, CichoĊ„ M et al. MHC diversity, malaria and lifetime reproductive success in collared flycatchers. Mol Ecol. 2012 May;21(10):2469-79. [Pubmed]
4 Herdegen M, Babik W, Radwan J. Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure. J Evol Biol. 2014 Nov;27(11):2347-59. [Pubmed]

Minimum amplicon depth: Amplicons with lower total coverage will be discarded.
Amplicon data: It is very important to specify all the primer and tag sequences in 5'->3' sense.
Shortening primer sequences to 7-9 nts can increase the number of retrieved sequences (eg. GAGTGTCAT instead of GAGTGTCATTTCTCCAACGGGA).

or file: Max. 100 KB See example

Alleles file (optional): FASTA format Max. 2 MB See example
Maximum number of reads per amplicon: Maximum number of amplicon sequences/reads to be processed.
Exact length required: Only sequences that satisfy theoretical marker lengths can be 'dominant' within a cluster.
In-frame length required: Only sequences in-frame with marker theoretical lengths can be 'dominant' within a cluster.


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